The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.
Positional Effect of Chemical Modifications on Short Interference RNA Activity in Mammalian Cells
Abstract
A systematic study on the effect of 2'-sugar modifications (2'-F (2'-F-2'-deoxy-nucleoside residues), 2'-O-Me (2'-O-methyl-nucleoside residues), and 2'-O-MOE [2'-O-(2-methoxyethyl)]-nucleoside residues) in the antisense and sense strands of short interference RNA (siRNA) was performed in HeLa cells. The study of the antisense strand of siRNAs demonstrated that activity depends on the position of the modifications in the sequence. The siRNAs with modified ribonucleotides at the 5'-end of the antisense strand were less active relative to the 3'-modified ones. The 2'-F sugar was generally well-tolerated on the antisense strand, whereas the 2'-O-Me showed significant shift in activity depending on the position of modification. The 2'-O-MOE modification in the antisense strand resulted in less active siRNA constructs regardless of placement position in the construct. The incorporation of the modified residues, e.g., 2'-O-Me and 2'-O-MOE, in the sense strand of siRNA did not show a strong positional preference. These results may provide guidelines to design effective and stable siRNAs for RNA interference mediated therapeutic applications.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998) · Nature · doi:10.1038/35888 · Cited by 15,429
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells
Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., & Tuschl, T. (2001) · Nature · doi:10.1038/35078107 · Cited by 9,456
Role for a bidentate ribonuclease in the initiation step of RNA interference
Bernstein, E., Caudy, A. A., Hammond, S. M., & Hannon, G. J. (2001) · Nature · doi:10.1038/35053110 · Cited by 4,892
RNA interference is mediated by 21- and 22-nucleotide RNAs
Elbashir, S. M., Lendeckel, W., & Tuschl, T. (2001) · Genes & Development · doi:10.1101/gad.862301 · Cited by 3,310
An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells
Hammond, S. M., Bernstein, E., Beach, D., & Hannon, G. J. (2000) · Nature · doi:10.1038/35005107 · Cited by 3,003
Argonaute2 is the catalytic engine of mammalian RNAi
Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G., Thomson, J. M., Song, J.-J., Hammond, S. M., Joshua-Tor, L., & Hannon, G. J. (2004) · Science · doi:10.1126/science.1102513 · Cited by 2,796
A novel method for real time quantitative RT-PCR.
Gibson, U. E., Heid, C. A., & Williams, P. M. (1996) · Genome Research · doi:10.1101/gr.6.10.995 · Cited by 2,075
Argonaute2, a Link Between Genetic and Biochemical Analyses of RNAi
Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R., & Hannon, G. J. (2001) · Science · doi:10.1126/science.1064023 · Cited by 1,580
Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity
Song, J.-J., Smith, S. K., Hannon, G. J., & Joshua-Tor, L. (2004) · Science · doi:10.1126/science.1102514 · Cited by 1,470
Single-Stranded Antisense siRNAs Guide Target RNA Cleavage in RNAi
Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R., & Tuschl, T. (2002) · Cell · doi:10.1016/s0092-8674(02)00908-x · Cited by 1,459
Winer, J., Jung, C. K. S., Shackel, I., & Williams, P. M. (1999) · Analytical Biochemistry · doi:10.1006/abio.1999.4085 · Cited by 1,387
Kennerdell, J. R., & Carthew, R. W. (1998) · Cell · doi:10.1016/s0092-8674(00)81725-0 · Cited by 1,132
Role of the histone deacetylase complex in acute promyelocytic leukaemia
Lin, R. J., Nagy, L., Inoue, S., Shao, W., Miller, W. H., & Evans, R. M. (1998) · Nature · doi:10.1038/35895 · Cited by 1,062
Caplen, N. J., Parrish, S., Imani, F., Fire, A., & Morgan, R. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171251798 · Cited by 1,043
ATP Requirements and Small Interfering RNA Structure in the RNA Interference Pathway
Nykänen, A., Haley, B., & Zamore, P. D. (2001) · Cell · doi:10.1016/s0092-8674(01)00547-5 · Cited by 1,016
Antisense technologies: Improvement through novel chemical modifications
Kurreck, J. (2003) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2003.03555.x · Cited by 1,006
Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells
Lee, N. S., Dohjima, T., Bauer, G., Li, H., Li, M.-J., Ehsani, A., Salvaterra, P., & Rossi, J. (2002) · Nature Biotechnology · doi:10.1038/nbt0502-500 · Cited by 953
siRNA function in RNAi: A chemical modification analysis
CHIU, Y.-L., & RANA, T. M. (2003) · RNA · doi:10.1261/rna.5103703 · Cited by 860
siRNA-directed inhibition of HIV-1 infection
Novina, C. D., Murray, M. F., Dykxhoorn, D. M., Beresford, P. J., Riess, J., Lee, S.-K., Collman, R. G., Lieberman, J., Shankar, P., & Sharp, P. A. (2002) · Nature Medicine · doi:10.1038/nm725 · Cited by 773
Transitions in Distinct Histone H3 Methylation Patterns at the Heterochromatin Domain Boundaries
Noma, K.-I., Allis, C. D., & Grewal, S. I. S. (2001) · Science · doi:10.1126/science.1064150 · Cited by 747
Modulation of HIV-1 replication by RNA interference
Jacque, J.-M., Triques, K., & Stevenson, M. (2002) · Nature · doi:10.1038/nature00896 · Cited by 719
Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells
Czauderna, F. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg393 · Cited by 623
Short interfering RNA confers intracellular antiviral immunity in human cells
Gitlin, L., Karelsky, S., & Andino, R. (2002) · Nature · doi:10.1038/nature00873 · Cited by 608
In vivo activity of nuclease-resistant siRNAs
LAYZER, J. M., MCCAFFREY, A. P., TANNER, A. K., HUANG, Z., KAY, M. A., & SULLENGER, B. A. (2004) · RNA · doi:10.1261/rna.5239604 · Cited by 580
Song, J.-J., Liu, J., Tolia, N. H., Schneiderman, J., Smith, S. K., Martienssen, R. A., Hannon, G. J., & Joshua-Tor, L. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb1016 · Cited by 575
Kinetic analysis of the RNAi enzyme complex
Haley, B., & Zamore, P. D. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb780 · Cited by 544
Tolerance for mutations and chemical modifications in a siRNA
Amarzguioui, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg147 · Cited by 534
RNA Interference in Mammalian Cells by Chemically-Modified RNA
Braasch, D. A., Jensen, S., Liu, Y., Kaur, K., Arar, K., White, M. A., & Corey, D. R. (2003) · Biochemistry · doi:10.1021/bi0343774 · Cited by 531
RNAi: nature abhors a double-strand
Hutvágner, G., & Zamore, P. D. (2002) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(02)00290-3 · Cited by 508
RNA Silencing: The Genome's Immune System
Plasterk, R. H. A. (2002) · Science · doi:10.1126/science.1072148 · Cited by 468
RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing
Ahlquist, P. (2002) · Science · doi:10.1126/science.1069132 · Cited by 462
Efficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents
Vickers, T. A., Koo, S., Bennett, C. F., Crooke, S. T., Dean, N. M., & Baker, B. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m210326200 · Cited by 461
Self-citation(1989) · Wills' Biochemical Basis of Medicine · doi:10.1016/b978-0-7236-0914-8.50061-5 · Cited by 446
Kawasaki, A. M., Casper, M. D., Freier, S. M., Lesnik, E. A., Zounes, M. C., Cummins, L. L., Gonzalez, C., & Cook, P. D. (1993) · Journal of Medicinal Chemistry · doi:10.1021/jm00059a007 · Cited by 438
Synthesis, deprotection, analysis and purification of RNA and ribosomes
Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., & Usman, N. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.14.2677 · Cited by 398
Chiu, Y.-L., & Rana, T. M. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00652-4 · Cited by 395
RNA interference: listening to the sound of silence.
Zamore, P. D. (2001) · Nature Structural Biology · doi:10.1038/nsb0901-746 · Cited by 372
Ancient Pathways Programmed by Small RNAs
Zamore, P. D. (2002) · Science · doi:10.1126/science.1072457 · Cited by 360
E3 ubiquitin ligase that recognizes sugar chains
Yoshida, Y., Chiba, T., Tokunaga, F., Kawasaki, H., Iwai, K., Suzuki, T., Ito, Y., Matsuoka, K., Yoshida, M., Tanaka, K., et al. (2002) · Nature · doi:10.1038/nature00890 · Cited by 350
Manoharan, M. (1999) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(99)00138-4 · Cited by 348
The RNA-Induced Silencing Complex Is a Mg2+-Dependent Endonuclease
Schwarz, D. S., Tomari, Y., & Zamore, P. D. (2004) · Current Biology · doi:10.1016/j.cub.2004.03.008 · Cited by 267
Biodistribution of phosphodiester and phosphorothioate siRNA
Braasch, D. A., Paroo, Z., Constantinescu, A., Ren, G., Öz, O. K., Mason, R. P., & Corey, D. R. (2004) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2003.12.074 · Cited by 251
Novel Antisense and Peptide Nucleic Acid Strategies for Controlling Gene Expression
Braasch, D. A., & Corey, D. R. (2002) · Biochemistry · doi:10.1021/bi0122112 · Cited by 248
Ein neuer Zugang zu 2′‐O‐Alkylribonucleosiden und Eigenschaften deren Oligonucleotide
Martin, P. (1995) · Helvetica Chimica Acta · doi:10.1002/hlca.19950780219 · Cited by 234
A genetic link between co-suppression and RNA interference in C. elegans
Ketting, R. F., & Plasterk, R. H. A. (2000) · Nature · doi:10.1038/35005113 · Cited by 214
Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide
Polacek, N., Gaynor, M., Yassin, A., & Mankin, A. S. (2001) · Nature · doi:10.1038/35078113 · Cited by 205
Small Interfering RNAs: A Revolutionary Tool for the Analysis of Gene Function and Gene Therapy
Tuschl, T. (2002) · Molecular Interventions · doi:10.1124/mi.2.3.158 · Cited by 185
Inhibition of Retroviral Pathogenesis by RNA Interference
Hu, W.-Y., Myers, C. P., Kilzer, J. M., Pfaff, S. L., & Bushman, F. D. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00975-2 · Cited by 181
Improvement through novel chemical modifications
Kurreck, J. (2003) · Cited by 179
A model for SOS-lesion-targeted mutations in Escherichia coli
Pham, P., Bertram, J. G., O’Donnell, M. E., Woodgate, R., & Goodman, M. F. (2001) · Nature · doi:10.1038/35053116 · Cited by 127
RNA interference: antiviral defense and genetic tool
Cullen, B. R. (2002) · Nature Immunology · doi:10.1038/ni0702-597 · Cited by 126
Hashimoto, J. G., Beadles-Bohling, A. S., & Wiren, K. M. (2004) · BioTechniques · doi:10.2144/04361bm06 · Cited by 114
A Conformationally Preorganized Universal Solid Support for Efficient Oligonucleotide Synthesis
Guzaev, A. P., & Manoharan, M. (2003) · Journal of the American Chemical Society · doi:10.1021/ja0284613 · Cited by 41
Cited by
Bennett, C. F., & Swayze, E. E. (2010) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.010909.105654 · Cited by 1,374
Self-citationThe chemical evolution of oligonucleotide therapies of clinical utility
Khvorova, A., & Watts, J. K. (2017) · Nature Biotechnology · doi:10.1038/nbt.3765 · Cited by 1,216
RNAi therapeutics: a potential new class of pharmaceutical drugs
Bumcrot, D., Manoharan, M., Koteliansky, V., & Sah, D. W. Y. (2006) · Nature Chemical Biology · doi:10.1038/nchembio839 · Cited by 1,085
Illuminating the silence: understanding the structure and function of small RNAs
Rana, T. M. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2085 · Cited by 1,083
siRNA versus miRNA as therapeutics for gene silencing
Lam, J. K. W., Chow, M. Y. T., Zhang, Y., & Leung, S. W. S. (2015) · Molecular Therapy — Nucleic Acids · doi:10.1038/mtna.2015.23 · Cited by 1,081
Metadata
- Authors
- Prakash, T. P., Allerson, C. R., Dande, P., Vickers, T. A., Sioufi, N., Jarres, R., Baker, B. F., Swayze, E. E., Griffey, R. H., & Bhat, B.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-05-27
- Volume
- 48
- Issue
- 13
- Pages
- 4247-4253
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W2168993612
- Cited by
- 285
- References
- 53
- FWCI
- 6.22
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
